MAQC papers over the cracks.
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Conflict of Interest↗
Biomedical subjects
Peng Liang
Publications and source records attributed to Peng Liang.
TIS11D is a candidate pro-apoptotic p53 target gene.
A number of target genes for the tumor suppressor, p53, have been identified, however, the mechanisms that contribute to p53-dependent apoptosis remain to be fully elucidated. In a comprehensive screen for p53 target genes by differential display, we have identified TIS11D as a p53-inducible gene. Induction of TIS11D mRNA was confirmed by Northern Blot in response to p53 expression. Inducible expression of TIS11D resulted in inhibition of cell proliferation and apoptosis. These data suggest TIS11D as a candidate p53 target gene that may be part of the network of genes responsible for p53-dependent apoptosis.
Animals↗
Human neural stem cells promote corticospinal axons regeneration and synapse reformation in injured spinal cord of rats.
BACKGROUND: Axonal regeneration in lesioned mammalian central nervous system is abortive, and this causes permanent disabilities in individuals with spinal cord injuries. This paper studied the action of neural stem cell (NSC) in promoting corticospinal axons regeneration and synapse reformation in rats with injured spinal cord. METHODS: NSCs were isolated from the cortical tissue of spontaneous aborted human fetuses in accordance with the ethical request. The cells were discarded from the NSC culture to acquire NSC-conditioned medium. Sixty adult Wistar rats were randomly divided into four groups (n = 15 in each): NSC graft, NSC medium, graft control and medium control groups. Microsurgical transection of the spinal cord was performed in all the rats at the T11. The NSC graft group received stereotaxic injections of NSCs suspension into both the spinal cord stumps immediately after transection; graft control group received DMEM injection. In NSC medium group, NSC-conditioned medium was administered into the spinal cord every week; NSC culture medium was administered to the medium control group. Hindlimb motor function was assessed using the BBB Locomotor Rating Scale. Regeneration of biotin dextran amine (BDA) labeled corticospinal tract was assessed. Differentiation of NSCs and the expression of synaptophysin at the distal end of the injured spinal cord were observed under a confocal microscope. Group comparisons of behavioral data were analyzed with ANOVA. RESULTS: NSCs transplantation resulted in extensive growth of corticospinal axons and locomotor recovery in adult rats after complete spinal cord transection, the mean BBB scores reached 12.5 in NSC graft group and 2.5 in graft control group (P < 0.05). There was also significant difference in BBB score between the NSC medium (11.7) and medium control groups (3.7, P < 0.05). BDA traces regenerated fibers sprouted across the lesion site and entered the caudal part of the spinal cord. Synaptophysin expression colocalized with BDA positive axons and neurons distal to the injury site. Transplanted cells were found to migrate into the lesion, but not scatter along the route of axon grows. The cells differentiated into astrocytes or oligodendrocytes, but not into the neurons after transplantation. Furthermore, NSC medium administration did not limit the degree of axon sprouting and functional recovery of the injured rats compared to the NSC graft group. CONCLUSIONS: Human embryonic neural stem cells can promote functional corticospinal axons regeneration and synapse reformation in the injured spinal cord of rats. The action is mainly through the nutritional effect of the stem cells on the spinal cord.
Animals↗
Excess sludge reduction induced by Tubifex tubifex in a recycled sludge reactor.
Sludge reduction in a conventional activated sludge (CAS) process combined with a recycled sludge reactor where Tubifex tubifex (one of Oligochaeta) was inoculated was investigated in this study. The results showed sludge production could be reduced through T. tubifex's predation on sludge in the recycled sludge reactor. The sludge reduction rate of T. tubifex (R) was from 0.18 to 0.81 mg-VSS mg-Tubifex(-1) d(-1). The sludge reduction capacity of the recycled sludge reactor E was from 650 to 1080 mg-VSS L(-1) d(-1). The optimum density of T. tubifex was 2500 mg L(-1) and the optimum sludge recycled ratio was 1. The existence of T. tubifex did not affect COD and NH(4)(+)-N removals in the process, but led to a slight decrease in TP removal. SVI almost did not change when the T. tubifex density was lower than 3300 mg L(-1). The LC50 values on T. tubifex of copper and ammonia were 2.5 and 880 mg L(-1), respectively, both of which were higher than those on Aeolosoma hemprichi.
Ammonia↗
From differential display to DNA microarrays--a personal account.
This article is a tribute to Dr. Arthur Pardee, one of the most innovative and brilliant scientists of our time, on the occasion of his 85th birthday. In this partially perspective and partially review piece, I look back how fate, by twist and turn, has led me eventually to his lab at Harvard where we worked out the Differential Display technology from scratch, how the method has revolutionized the field of gene expression analysis and where DD is taking us in the "era" of DNA microarrays.
Gene Expression Profiling↗
Cation-controlled aqueous dispersions of alginic-acid-wrapped multi-walled carbon nanotubes.
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Alginates↗
Quality and stability analysis for the rainfall water and surface runoff water in southeast region of Beijing Municipality.
In this study, water sampling was carried out extensively through collection of natural rainfall and municipal surface runoff water samples in the southeast region of Beijing Municipality during the period of June 2002 to July 2004. Chemical tests and measurements of collected water samples were conducted in the laboratory in order to evaluate rainwater quality and to analyze chemical stability of rainwater. The test results show that the collected rainfall water and surface runoff water were soft water and belonged to bicarbonate-calcium Type-I water category. The results also show that their pH levels were closely related to the strength of alkaline constituents in the rainwater. Water quality analysis indicated that the rainwater collected from the study region had been contaminated to a certain degree by nitrogen and organic compounds from intensive human activities. Water stability analysis focuses mainly on the potential of precipitation-dissolution of carbonate calcium (CaCO3). The results show that only the rainwater samples collected from traffic roads were oversaturated with respect to CaCO3 and had a tendency to precipitate, while other rainwater samples were unsaturated with respect to CaCO3 and had the potential to keep dissolving CaCO3 into rainwater. The results obtained in this study may help to develop better rainwater utilization strategies for alleviating the growing water shortage pressure faced by the City of Beijing.
Calcium↗
Global analysis of gene expression by differential display: a mathematical model.
Differential display (DD) is one of the most commonly used approaches for identifying differentially expressed genes. However, there has been lack of an accurate guidance on how many DD polymerase chain reaction (PCR) primer combinations are needed to display most of the genes expressed in a eukaryotic cell. This study critically evaluated the gene coverage by DD as a function of the number of arbitrary primers, the number of 3' bases of an arbitrary primer required to completely match an mRNA target sequence, the additional 5' base match(s) of arbitrary primers in first-strand cDNA recognition, and the length of mRNA tails being analyzed. The resulting new DD mathematical model predicts that 80-160 arbitrary 13mers, when used in combinations with three one-base anchored oligo-dT primers, would allow any given mRNA within a eukaryotic cell to be detected with a 74-93% probability, respectively. The prediction was supported by both computer simulation of the DD process and experimental data from a comprehensive fluorescent DD screening for target genes of tumor-suppressor p53. Thus, this work provides a theoretical foundation upon which global analysis of gene expression by DD can be pursued.
Base Sequence↗
Automation of fluorescent differential display with digital readout.
Since its invention in 1992, differential display (DD) has become the most commonly used technique for identifying differentially expressed genes because of its many advantages over competing technologies such as DNA microarray, serial analysis of gene expression (SAGE), and subtractive hybridization. Despite the great impact of the method on biomedical research, there has been a lack of automation of DD technology to increase its throughput and accuracy for systematic gene expression analysis. Most of previous DD work has taken a "shot-gun" approach of identifying one gene at a time, with a limited number of polymerase chain reaction (PCR) reactions set up manually, giving DD a low-tech and low-throughput image. We have optimized the DD process with a new platform that incorporates fluorescent digital readout, automated liquid handling, and large-format gels capable of running entire 96-well plates. The resulting streamlined fluorescent DD (FDD) technology offers an unprecedented accuracy, sensitivity, and throughput in comprehensive and quantitative analysis of gene expression. These major improvements will allow researchers to find differentially expressed genes of interest, both known and novel, quickly and easily.
Automation↗
Saturation screening for p53 target genes by digital fluorescent differential display.
Differential display (DD) is one of the most commonly used approaches for identifying differentially expressed genes. Despite the great impact of the method on biomedical research, there has been a lack of automation of DD technology to increase its throughput and accuracy for a systematic gene expression analysis. Most of previous DD work has taken a "shotgun" approach of identifying one gene at a time, with limited polymerase chain reaction (PCR) reactions set up manually, giving DD a low-technology and low-throughput image. With our newly created DD mathematical model, which has been validated by computer simulations, global analysis of gene expression by DD technology is no longer a shot in the dark. After identifying the "rate-limiting" factors that contribute to the "noise" level of DD method, we have optimized the DD process with a new platform that incorporates fluorescent digital readout and automated liquid handling. The resulting streamlined fluorescent DD (FDD) technology offers an unprecedented accuracy, sensitivity, and throughput in comprehensive and quantitative analysis of gene expression. We are using this newly integrated FDD technology to conduct a systematic and comprehensive screening for p53 tumor-suppressor gene targets.
Animals↗
Identification by differential display of IL-24 autocrine loop activated by ras oncogenes.
Ras signaling pathway is thought to control the expression of a subset of yet-to-be-defined genes that are crucial for cell growth and differentiation. Here we have identified by differential display a novel oncogenic Ras target gene encoding a new cytokine. Biochemical studies reveal that this cytokine, which we named IL-24, is a member of IL-10 family of cytokines, and it signals through two hetorodimeric receptors, whose expression is also upregulated by ras oncogenes. Thus, IL-24 and its receptors may represent a novel autocrine loop coordinately activated by ras oncogenes.
Blotting, Western↗
Detection of an mRNA polymorphism by differential display.
Differential display technology was utilized to compare programs of gene expression in primary cultures of human skin fibroblasts from normal volunteers and patients diagnosed with melancholic depression. Polymorphic transcripts of a single gene differing by one tandem repeat sequence of four nucleotides (TGAT) in the 3' noncoding region were detected.
Base Sequence↗
[Novel SCN5A gene mutations associated with Brugada syndrome: V95I, A1649V and delF1617].
OBJECTIVE: Brugada syndrome is an inherited channelopathy that characterized by ST-segment elevation in the right precordial lead (V(1)-V(3)) on the electrocardiogram with or without right bundle branch block and related with high risk of sudden cardiac death and structurally normal hearts. The first and only gene linked to this disease is SCN5A, a gene encodes for alpha subunit of the cardiac sodium channel. The objective of this study is to explore SCN5A gene mutations in Chinese patients with Brugada syndrome. METHODS: Four patients diagnosed as Brugada syndrome and nine patients with suspected Brugada syndrome were chosen for the study. The exons in the functional regions of SCN5A gene were amplified with polymerase chain reaction and the amplified products were sequenced with Sanger method. If a mutation was identified, patient's family members were also screened. RESULTS: Two heterozygous mutations were found in one family diagnosed as Brugada syndrome. One missense mutation was a G-->A transition in the first nucleotide of codon 95 in SCN5A gene exon 3, which was predicted to result in substitution of Valine with Isoleucine (V95I). The other missense mutation was a C-->T transition in the second nucleotide of codon 1649 in SCN5A gene exon 28, which was predicted to result in substitution of Alanine with Valine (A1649V). A heterozygous mutation was identified in one family suspected to have the disease. The mutation was a three nucleotides (TCT) deletion that caused Phenylalanine deletion in codon 1617 in SCN5A gene exon 28. The three mutations were not detected in 100 control chromosomes. CONCLUSIONS: Mutation in SCN5A gene is one of the causes of Brugada syndrome in Chinese. Three novel SCN5A gene mutations were identified in Chinese with Brugada syndrome, which expands the spectrum of SCN5A mutations associated with the disease.
Adolescent↗
Spectrophotometric study of fluorescence sensing and selective binding of biochemical substrates by 2,2'-bridged bis(beta-cyclodextrin) and its water-soluble fullerene conjugate.
A bis(beta-cyclodextrin)-fullerene conjugate (3) linked at the secondary hydroxyl side was prepared in a good yield from its precursor N,N'-bis(2-(2-aminoethylamino)ethyl)malonamide-bridged bis(beta-cyclodextrin) (2). Spectrophotomeric studies on the conformation and the inclusion complexation behavior of 3 with a variety of organic and biochemical substrates by means of UV-vis, FT-IR, NMR, fluorescence, and circular dichroism spectroscopy showed that the bis(beta-cyclodextrin)-fullerene conjugate displayed an intramolecular capsule-type conformation in aqueous solution. Because of the multiple binding of bis(beta-cyclodextrin) with substrates, 2 can act as an efficient fluorescence sensor for biochemical substrates, while its fullerene conjugate 3 displays a capability of cleaving DNA under visible-light irradiation.
Benzyl Compounds↗
Determination and comparison of sludge reduction rates caused by microfaunas' predation.
Using micorfauna to reduce excess sludge is a potentially effective ecological technology and scaling the rate of sludge reduction rate is the first step. A method to scale the rate of sludge reduction caused by microfauna was proposed, and comparison of sludge reduction rates induced by four microfaunas was carried out. The principle of this method is based on the change of carbon forms. The rate of sludge reduction was correlated with the rate at which solids were changed into liquid and gas. Four microfaunas, including Aeolosoma hemprichi, Daphnia magna, Tubifex tubifex and Physa acuta, were cultured with sterilized sludge in a covered sterilized bottle and were then isolated from the atmosphere above the liquid phase. The rates of sludge reduction using the four microfaunas were 0.8, 0.18, 0.54 and 0.1 mg-sludge/(mg-Microfauna d), respectively, changing with the microfaunas' phylum or class and body size. Based on the change of carbon (C) forms, the proposed method produced accurate results similar to those produced using the direct measuring method.
Animals↗
Endo180 binds to the C-terminal region of type I collagen.
Type I collagen is a fibril-forming heterotrimer composed of two alpha1 and one alpha2 chains and plays a crucial role in cell-matrix adhesion and cell differentiation. Through a comprehensive differential display screening of oncogenic ras target genes, we have shown that the alpha1 chain of type I collagen (col1a1) is markedly down-regulated by the ras oncogene through the mitogen-activated protein kinase pathway. Although ras-transformed cells are no longer able to produce and secrete endogenous collagen, they can still adhere to exogenous collagen, suggesting that the cells express a collagen binding factor(s) on the cell surface. When the region of col1a1 encompassing the C-terminal glycine repeat and C-prodomain (amino acids 1000-1453) was affinity-labeled with human placental alkaline phosphatase, the secreted trimeric fusion protein could bind to the surface of Ras-transformed cells. Using biochemical purification followed by matrix-assisted laser desorption/ionization mass spectrometry analysis, we identified this collagen binding factor as Endo180 (uPARAP, CD280), a member of the mannose receptor family. Ectopic expression of Endo180 in CosE5 cells followed by in situ staining and quantitative binding assays confirmed that Endo180 indeed recognizes and binds to placental alkaline phosphatase. The interaction between Endo180 and the C-terminal region of type I collagen appears to play an important role in cell-matrix adhesion.
Alkaline Phosphatase↗
Interleukin-24 and its receptors.
Interleukin 24 (IL-24) is a new member of the IL-10 family of cytokines and it signals through two heterodimeric receptors: IL-20R1/IL-20R2 and IL-22R1/IL-20R2. Upon binding to its receptors, IL-24 induces rapid activation of Stat-1 and Stat-3 transcription factors, which appear to play a role in cell survival and proliferation. Under physiological conditions, the major sources of IL-24 are the activated monocytes and T helper 2 cells, whereas the major IL-24 target tissues, based on the receptor expression pattern, are non-haematopoietic in origin, and include skin, lung and reproductive tissues. Structurally and functionally, IL-24 is highly conserved across species. This review highlights our current knowledge of IL-24 as a cytokine, with much less emphasis placed on the non-receptor-mediated functions (a subject of several reviews) focused on in much of the earlier literature on IL-24. The potential roles of IL-24 as part of a complex cytokine network in wound healing, psoriasis and cancer are discussed.
Cell Proliferation↗
[Effects of sucrose and light on the growth and production of secondary metabolites in Pueraria phaseoloides hairy roots].
Effects of sucrose concentrations and light on the growth and production of total isoflavones and puerarin in Pueraria phaseoloides hairy roots cultured onto solid MS media supplemented with 1%, 3%, 5%, 7% and 9% sucrose, respectively, were investigated. The results showed that among the sucrose concentrations tested, 3% sucrose in the medium enhanced the growth and stimulated accumulation of total isoflavones and puerarin in P. phaseoloides hairy roots, After cultured for 20 days, the biomass of hairy roots reached 0.48 g (DW dry weight)/flask and its contents of total isoflavones and puerarin were 25.44 mg/g (DW) and 11.64 mg/g (DW), respectively. In comparison with 3% sucrose, the dry weight proliferation of hairy roots cultured with 5% sucrose was increased by 7.0%, while cultured with 1%, 7% and 9% sucrose, the dry weight proliferation of hairy roots was decreased by 62.4%, 42.8% and 65.3%, their total isoflavones content was decreased by 57.4%, 13% and 33.4% and their puerarin content was decreased by 47.9%, 15.8% and 35.1%; but their content of total soluble sugars was increased 0.52, 1.45 and 1.54 times, respectively. Compared with hairy roots in blue light and white light, the biomass of hairy roots cultured in the dark for 30 days was 0.83 g (DW)/flask and was increased by 37.1% and 23.3%, respectively. The content of total isoflavones in hairy roots cultured in white light was as much as 1.15 times and 1.19 times that in blue light and in the dark, respectively. It was also observed that hairy roots cultured in blue light and white light partly became light green and that blue light could inhibit accumulation of puerarin in hairy roots and the puerarin content in hairy root cultured in white light and in the dark were 1.61 times and 1.52 times that in blue light, respectively.
Culture Media↗